| Category | Tool | Icon | Function | How to Access | Help Page |
|---|---|---|---|---|---|
| Quality Assessment | Assess Array Quality for an Array List | Calculate a "Q-score" (quality score) for a set of experiments based on a genelist | from "Lists" -> "All programs" -> "Tools" | YES | |
| Compare replicate arrays | Compare the measured data between two replicate experiments | from "Search" -> "Advanced Results Search"-> "Display Data" -> "View Array Details" icon -> "Compare measurements with an experiment from the same Print" | YES | ||
| Get Ratios on Array | Investigate spatial location or plate bias on an array | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon -> "Ratios on Array" | YES (included in program text) |
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| Data Plotter |  |
Plot data from a selected experiment or set of experiments as a scatter plot or histogram. Can select any two parameters to plot. | from "Search" -> "Advanced Results Search" (or "Basic Search" -> "Display Data") -> "Display Data" -> "Plot Array Data" icon or "View Array Details" icon -> "Plot Data" or "Signal Intensities" | YES |
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| Plot Data Distribution | Make a histogram of log2(RAT2N) for one experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon or "Edit" icon -> "(View) Data Distribution" | |||
| Clustering and other Data Analysis | Cluster Data |  |
Filter and organize data using hierarchical clustering or self organizing maps | from "Search" -> "Advanced Results Search" ->"Data Retrieval and Analysis" -> select experiments -> "Data Retrieval and Analysis" | YES |
| Reenter Data Clustering Pipeline |  |
Reenter the data clustering pipeline starting with a repository file | from "My Repository" -> click on icon | YES | |
| Synthetic Genes |  |
Add annotations or combine expression data from a group of reporters (e.g. for clustering) | from "My Data" -> "My Repository" -> click on icon (input is a .pcl file) | YES | |
| KNNimpute |  |
Impute values for missing data | from "My Data" -> "My Repository" -> click on icon | YES | |
| GeneXplorer |  |
Interactively view clustered data | from "My Data" -> "My Repository" -> click on icon | ||
| TreeView | Graphically browse results of clustering and other analyses from Cluster | Download software from Eisen Lab (requires .cdt and .gpr files) |
YES(intrinsic) | ||
| Singular Value Decomposition (SVD) |  |
Identify patterns (real experimental results or artifacts) in a data set | from "My Data" -> "My Repository" -> click on icon | YES | |
| Merge PCL files | Merge PCL files (e.g. for co-clustering data or for adding clinical values to gene expression data) | from "List all Programs" -> "Tools" | YES | ||
| Data Viewing/Visualization | GeneXplorer | |
Interactively view clustered data | from "My Data" -> "My Repository" -> click on icon | |
| Ontology Term Finder (GO::TermFinder) | Identify Gene Ontology terms for a group of genes that annotate that group in a statistically significant manner. This can help one discover what biological processes, cellular localizations or molecular functions are shared by members of groups of genes. | from Main Tool Menu Bar or from "Lists" -> "All programs" -> "Tools" | YES | ||
| Data Plotter | |
Plot data from a selected experiment or set of experiments as a scatter plot or histogram. Can select any two parameters to plot. | from "Search" -> "Advanced Results Search" (or "Basic Search" -> "Display Data") -> "Display Data" -> "Plot Array Data" icon or "View Array Details" icon -> "Plot Data" or "Signal Intensities" | YES |
|
| Plot Data Distribution | Make a histogram of log2(RAT2N) for one experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon or "Edit" icon -> "(View) Data Distribution" | |||
| TreeView | Graphically browse results of clustering and other analyses from Cluster | Download software from Eisen Lab (requires .cdt and .gpr files) |
YES(intrinsic) | ||
| View Array Images and Grids |  |
Select various criteria for filtering; then display the array image with selected spots boxed. Can also click on spots to get spot data | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | ||
| Get Spot Data (= View Array Images) |
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Obtain biological information and data from hybridization for a particular spot in one experiment. Can use to change flagging of spot. Similar to "View Array Images and Grids", but can select only one spot | from "Search" -> "Advanced Results Search" -> "Display Data" -> ("View and Sort Array Data" icon -> "Display Data" -> "Zoom") or from Grids icon | ||
| View Array Details |  |
Display Metadata about one experiment | from "Search" ->"Advanced Results Search" -> "Display Data" -> click on icon | ||
| View and Sort Array Data |  |
Sort data from one experiment by a selection of criteria. After sorting, can view individual spots in array context. | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | ||
| Data Transformation | Synthetic Genes | |
Add annotations or combine expression data from a group of reporters (e.g. for clustering) | from "My Data" -> "My Repository" -> click on icon (input is a .pcl file) | YES |
| KNNimpute | |
Impute values for missing data | from "My Data" -> "My Repository" -> click on icon | YES | Renormalize an Experiment or all Experiments using a Result Set List | Renormalize one or several results sets (arrays) with a variety of algorithms. | from "Search" -> "Advanced Results Search" -> "Display Data" -> "Edit" icon -> "Select normalization options" or ("Lists" -> "All Programs" -> "Edit/Delete Data" -> "Batch Renormalize Data") | YES |
| Renormalize Experiments using a Genelist | Calculate a normalization constant based on a restricted list of genes. Does not actually alter data | from "Lists" -> "All programs" -> "Tools" | YES | Background Correction for single Experiment or Experiments in a Result Set List | Use different spot backgrounds for one or several results sets (arrays) with a variety of algorithms. | from "Search" -> "Advanced Results Search" -> "Display Data" -> "Edit" icon -> "Select normalization options" or ("Lists" -> "All Programs" -> "Edit/Delete Data" -> "Batch Renormalize Data") | YES |
| Data Organization or Annotation | Create an Experiment Set | Compile selected experiments into a set that can be easily shared or published. | from "Search" -> "Advanced Search" -> "Data Retrieval and Analysis" -> "Create Experiment Set" | YES | |
| Create a Result Set | Compile selected arrays into a set. The results from one set of arrays can be processed into different result sets. | from "Search" -> "Advanced Search" -> "Data Retrieval and Analysis" -> "Create Result Set List" | YES | ||
| Convert an Arraylist to an Experiment Set | Convert an Array list to an Experiment set | from Main Tool Menu Bar or from "Lists" -> "All programs" -> "Tools" | YES | ||
| Delete Experiment |  |
Remove experiment from the database | from "Search" -> "Advanced Results Search" -> "Display Data" ->click on icon | YES | |
| Edit Experimental Data |  |
Edit MetaData about experiments | from "Search" -> "Advanced Results Search" ->"Display Data"->click on icon | ||
| Associate Patient Information | Associate clinical(patient and sample) information with an experiment | from "Search" -> "Advanced Results Search" -> "Display Data" ->"Edit" icon -> "Associate Patient Information" or "Associate Clinical Information" | |||
| Enter Protocol | Enter a new protocol and its details | from "My Data" -> "Add Protocol" | YES | ||
| Enter Experiment Annotation by Batch | Add Experiment annotation to multiple experiments at once via a batch file | from "My Data"->"Procedural Information" | YES | ||
| View Array Details | |
Display Metadata about one experiment | from "Search" ->"Advanced Results Search" -> "Display Data" -> click on icon | ||
| Merge PCL files | Merge PCL files (e.g. for co-clustering data or for adding clinical values to gene expression data) | from "List all Programs" -> "Tools" | YES | ||
| Entering Microarray Data and Array Designs | Enter an Experiment | Upload (from loader account)results from an experiment. Can also be uploaded in batch | from "My Data" -> "Enter my Data" | YES | |
| Create a Result Set | Compile selected arrays into a set. The results from one set of arrays can be processed into different result sets. | from "Search" -> "Advanced Search" -> "Data Retrieval and Analysis" -> "Create Result Set List" | YES | ||
| Upload Gif | Upload (from loader account) a GIF file for a particular experiment | from "My Data" -> "Upload GIF" | YES | ||
| Enter Protocol | Enter a new protocol and its details | from "My Data" -> "Add Protocol" | YES | ||
| Associate Patient Information | Associate clinical(patient and sample) information with an experiment | from "Search" -> "Advanced Results Search" -> "Display Data" ->"Edit" icon -> "Associate Patient Information" or "Associate Clinical Information" | |||
| Enter Experiment Annotation by Batch | Add Experiment annotation to multiple experiments at once via a batch file | from "My Data"->"Procedural Information" | YES | ||
| Godlist Validator("Validate a list of Plate Samples") | Format a list of plate samples("godlist") in proper format for print entry into SMD | from "Lists" -> "All programs" -> "Tools" | YES | ||
| Data Download | Download Raw Data |  |
Obtain all raw data from one experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | |
| Download Original Data |  |
Download all original data files for an experiment | from "Search" -> "Advanced Results Search" -> "Display Data" -> click on icon | ||
| Generate Chromosome-Aligned Data for Caryoscope |  |
Generate chromosome-aligned representation of data for use with Caryoscope | from "Search" -> "Advanced Results Search" -> "Display Data" ->click on icon | Caryoscope home | |
| Download Raw Data for a Result Set List | Retrieve raw data for a set of experiments(up to 50). Results go to an archive and are retrieved in compressed form. | from "Lists" -> "All programs" -> "Tools" | |||
| Get Gal File | Obtain a gal file for a particular print | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View Array Details" icon -> "GAL file" | |||
| Data Search and Retrieval | Ontology Browser (amiGO) | Search GO (Gene Ontology) by GO term (or a portion thereof) or by a gene product. The results include the GO hierarchy for the term, definition and synonyms for the term, external links, and the complete set of gene product associations for the term and any of its children. | "Tools" -> "Ontology Browser" | YES | |
| Get Spot History | Obtain a compilation of the expression level of the clone specified in all microarray experiments to which you have access | from "Search" -> "Advanced Results Search" -> "Display Data" -> "View and Sort Array Data" icon -> "Display Data" -> "Spot History" or starting from Name Search -> search for name-> "View Expression History" | YES | ||
| Name Search | Find data on a particular entity by "name". View data on the entity for all experiments to which you have access. Can link to expression history | from "Search" -> "Name Search" | YES | ||
| Retrieve all public data for an organism | Retrieve all public data for an organism | Browse directly to FTP site or link to the FTP site from Public Data Retrieval Help | YES | ||
| Retrieve Experiment Meta Data for an Arraylist | Retrieve and print to a downloadable file some Meta Data for each experiment in an Arraylist | from "Lists"->"All programs" -> "Tools" | |||
| Genomic Alignment | Enter cloneID, gene name, accession number, gene symbol or cytoband position and find the genomic alignment as given by goldenPath at UCSC | from "Lists"->"All programs" -> "Tools" | YES | ||
| Data Access | Edit Experimental Data | |
Edit MetaData about experiments(including Access privileges) | from "Search" -> "Advanced Results Search" ->"Display Data"->click on icon | |
| Add Data Access by Batch | Give user or group access to a batch of experiments via an array list | from list of all programs | |||
| Change Password | Change your SMD/Loader Password | from Main Tool Menu Bar or from "Lists" -> "All programs" -> "Tools" |